Variant report

Variant	rs2501343
Chromosome Location	chr1:159794576-159794577
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159793598..159795124-chr1:159893329..159895732,2	K562	blood:
2	chr1:159794122..159796114-chr1:159799555..159801580,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158714	Chromatin interaction
ENSG00000158710	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11585055	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11585323	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11585836	0.82[EUR][1000 genomes]
rs11586456	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11586557	1.00[JPT][hapmap]
rs11586788	1.00[JPT][hapmap]
rs11587247	1.00[JPT][hapmap]
rs11590961	0.82[EUR][1000 genomes]
rs11591079	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs2494495	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494519	0.85[EUR][1000 genomes]
rs2501344	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4443889	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4656851	0.84[EUR][1000 genomes]
rs55650803	0.82[EUR][1000 genomes]
rs57198275	0.82[EUR][1000 genomes]
rs58240276	0.82[EUR][1000 genomes]
rs6427496	0.83[CEU][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs6656979	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6657365	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs6672434	0.81[EUR][1000 genomes]
rs7519854	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv521503	chr1:159762120-159795478	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2501343	COPA	cis	cerebellum	SCAN
rs2501343	OLFML2B	cis	cerebellum	SCAN
rs2501343	FCRL6	cis	multi-tissue	Pritchard
rs2501343	OR6N2	cis	cerebellum	SCAN
rs2501343	HAPLN2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159774800-159796000	Weak transcription	Right Atrium	heart
2	chr1:159779600-159794800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:159791000-159795800	Enhancers	Primary T cells fromperipheralblood	blood
4	chr1:159791000-159796600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:159792000-159796000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:159792400-159796600	Enhancers	Placenta	Placenta
7	chr1:159793000-159799000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:159793400-159795600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:159793400-159796000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr1:159793400-159799800	Weak transcription	Lung	lung
11	chr1:159793600-159794600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:159793600-159795200	Weak transcription	Spleen	Spleen
13	chr1:159793600-159797000	Weak transcription	Gastric	stomach
14	chr1:159793800-159795000	Weak transcription	HSMMtube	muscle
15	chr1:159793800-159796800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr1:159793800-159798800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:159794000-159794800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:159794000-159795600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:159794000-159807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:159794200-159794600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:159794200-159794600	Weak transcription	Esophagus	oesophagus
22	chr1:159794200-159795200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:159794200-159804600	Weak transcription	Fetal Intestine Small	intestine
24	chr1:159794400-159796200	Enhancers	Primary neutrophils fromperipheralblood	blood

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